{ "type": "genome", "identifier": "GCF_000576595.1", "organism": "Intrasporangium oryzae NRRL B-24470", "title": "Intrasporangium oryzae NRRL B-24470", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Huazhong Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000576595.1", "bioproject": "PRJNA224116", "biosample": "SAMN02952955", "wgs_master": "AWSA00000000.1", "refseq_category": "reference genome", "taxid": "1386089", "species_taxid": "412687", "organism_name": "Intrasporangium oryzae NRRL B-24470", "infraspecific_name": "strain=NRRL B-24470", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/02/24", "asm_name": "genome", "asm_submitter": "Huazhong Agricultural University", "gbrs_paired_asm": "GCA_000576595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/576/595/GCF_000576595.1_genome", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4636528", "genome_size_ungapped": "4636528", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "140", "contig_count": "140", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000576595.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4332", "protein_coding_gene_count": "4216", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-02-24", "dateModified": "2014-02-24", "datePublished": "2014-02-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Intrasporangium oryzae NRRL B-24470" ], "sample_taxid": [ "1386089" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: Saitama Prefecture" ], "sample_host_location_id": [], "data_size": "1.241 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4636528", "Number of Sequences": "140", "Longest Sequences (bp)": "196110", "N50 (bp)": "80706", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.4", "Number of CDSs": "4207", "Average Protein Length": "323.9", "Coding Ratio (%)": "88.2", "Number of rRNAs": "2", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Intrasporangium calvum", "strain": "strain=DSM 43043", "accession": "GCA_000184685.1", "taxid": 53358, "species_taxid": 53358, "relation_to_type": "type", "validated": true, "ani": 81.4014, "matched_fragments": 743, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Intrasporangium chromatireducens", "strain": "strain=Q5-1", "accession": "GCA_000576575.1", "taxid": 1386088, "species_taxid": 1386088, "relation_to_type": "type", "validated": true, "ani": 81.1614, "matched_fragments": 648, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Knoellia flava", "strain": "strain=CGMCC 1.10749", "accession": "GCA_014636255.1", "taxid": 913969, "species_taxid": 913969, "relation_to_type": "type", "validated": true, "ani": 79.9702, "matched_fragments": 558, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Knoellia flava", "strain": "strain=TL1", "accession": "GCA_000768675.1", "taxid": 913969, "species_taxid": 913969, "relation_to_type": "type", "validated": true, "ani": 79.9132, "matched_fragments": 550, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Knoellia remsis", "strain": "strain=ATCC BAA-1496", "accession": "GCA_003002895.1", "taxid": 407159, "species_taxid": 407159, "relation_to_type": "type", "validated": true, "ani": 79.6545, "matched_fragments": 506, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phycicoccus jejuensis", "strain": "strain=NRRL B-24460", "accession": "GCA_000720925.1", "taxid": 367299, "species_taxid": 367299, "relation_to_type": "type", "validated": true, "ani": 79.6263, "matched_fragments": 593, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedococcus cremeus", "strain": "strain=CGMCC 1.6963", "accession": "GCA_900111375.1", "taxid": 587636, "species_taxid": 587636, "relation_to_type": "type", "validated": true, "ani": 79.4828, "matched_fragments": 621, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter indicus", "strain": "strain=CGMCC 1.12511", "accession": "GCA_900176385.1", "taxid": 857417, "species_taxid": 857417, "relation_to_type": "type", "validated": true, "ani": 79.2806, "matched_fragments": 467, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter endophyticus", "strain": "strain=YIM B02568", "accession": "GCA_016888335.1", "taxid": 2806261, "species_taxid": 2806261, "relation_to_type": "type", "validated": true, "ani": 79.2316, "matched_fragments": 459, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter terrae", "strain": "strain=NBRC 107853", "accession": "GCA_001591405.1", "taxid": 103817, "species_taxid": 103817, "relation_to_type": "type", "validated": true, "ani": 79.1736, "matched_fragments": 459, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter melonis", "strain": "strain=NBRC107855", "accession": "GCA_020567375.1", "taxid": 262209, "species_taxid": 262209, "relation_to_type": "type", "validated": true, "ani": 79.1002, "matched_fragments": 502, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter massiliensis", "strain": "strain=Marseille-P4121", "accession": "GCA_900289115.1", "taxid": 2058291, "species_taxid": 2058291, "relation_to_type": "type", "validated": true, "ani": 79.0075, "matched_fragments": 379, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter hoylei", "strain": "strain=PVAS-1", "accession": "GCA_004025845.1", "taxid": 364298, "species_taxid": 364298, "relation_to_type": "type", "validated": true, "ani": 78.8463, "matched_fragments": 459, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arsenicicoccus bolidensis", "strain": "strain=DSM 15745", "accession": "GCA_000426385.1", "taxid": 229480, "species_taxid": 229480, "relation_to_type": "type", "validated": true, "ani": 78.6947, "matched_fragments": 463, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arsenicicoccus cauae", "strain": "strain=MKL-02", "accession": "GCA_009707125.1", "taxid": 2663847, "species_taxid": 2663847, "relation_to_type": "type", "validated": true, "ani": 78.529, "matched_fragments": 445, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteipulveratus halotolerans", "strain": "strain=C296001", "accession": "GCA_001247745.1", "taxid": 1631356, "species_taxid": 1631356, "relation_to_type": "type", "validated": true, "ani": 78.3569, "matched_fragments": 498, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinimicrobium sediminis", "strain": "strain=EGI L100131", "accession": "GCA_021272345.1", "taxid": 2904603, "species_taxid": 2904603, "relation_to_type": "type", "validated": true, "ani": 77.9827, "matched_fragments": 354, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinotalea solisilvae", "strain": "strain=KACC 19191", "accession": "GCA_016464425.1", "taxid": 2072922, "species_taxid": 2072922, "relation_to_type": "type", "validated": true, "ani": 77.2663, "matched_fragments": 429, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudokineococcus lusitanus", "strain": "strain=CECT 7306", "accession": "GCA_003751265.1", "taxid": 763993, "species_taxid": 763993, "relation_to_type": "type", "validated": true, "ani": 77.0827, "matched_fragments": 440, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas telluris", "strain": "strain=CPCC 204705", "accession": "GCA_004886325.1", "taxid": 2306636, "species_taxid": 2306636, "relation_to_type": "type", "validated": true, "ani": 76.8525, "matched_fragments": 383, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas hominis", "strain": "strain=DSM 9581", "accession": "GCA_014201095.1", "taxid": 156981, "species_taxid": 156981, "relation_to_type": "suspected-type", "validated": true, "ani": 76.7863, "matched_fragments": 380, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas hominis", "strain": "strain=NBRC 16055", "accession": "GCA_007989225.1", "taxid": 156981, "species_taxid": 156981, "relation_to_type": "suspected-type", "validated": true, "ani": 76.7862, "matched_fragments": 373, "total_fragments": 1486, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000576595.1", "gtdb_species": "s__Humihabitans oryzae", "ani": 100.0, "matched_fragments": 1481, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "conclusive" }, { "accession": "GCF_001429185.1", "gtdb_species": "s__Terrabacter sp001429185", "ani": 83.3896, "matched_fragments": 961, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "99.06", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014646815.1", "gtdb_species": "s__Terrabacter tumescens", "ani": 83.3634, "matched_fragments": 952, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007991735.1", "gtdb_species": "s__Terrabacter aerolatus", "ani": 83.2534, "matched_fragments": 935, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001428505.1", "gtdb_species": "s__Terrabacter sp001428505", "ani": 83.2421, "matched_fragments": 963, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.23", "min_intra_species_ani": "99.23", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000383675.1", "gtdb_species": "s__Terrabacter sp000383675", "ani": 83.238, "matched_fragments": 974, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_006717145.1", "gtdb_species": "s__Humibacillus xanthopallidus_A", "ani": 83.118, "matched_fragments": 996, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_006716915.1", "gtdb_species": "s__Terrabacter sp006716915", "ani": 82.9905, "matched_fragments": 965, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_000955875.1", "gtdb_species": "s__Terrabacter sp000955875", "ani": 82.9851, "matched_fragments": 933, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001956915.1", "gtdb_species": "s__Monashia flava", "ani": 82.6333, "matched_fragments": 785, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_013361975.1", "gtdb_species": "s__Terrabacter sp013361975", "ani": 82.4496, "matched_fragments": 547, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "98.02", "mean_intra_species_af": "0.74", "min_intra_species_af": "0.70", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003635045.1", "gtdb_species": "s__Terracoccus luteus", "ani": 81.7908, "matched_fragments": 784, "total_fragments": 1486, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.59", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 24.0, "optimum_ph": 8.0, "genome_size": 4636528.0, "gc_content": 71.391, "coding_genes": 3536.5, "rRNA16S_genes": 2.0, "tRNA_genes": 48.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Intrasporangium", "oryzae", "NRRL", "B-24470" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }